cb95ab0ac3de81c54babc8b9ba1326d93901ad96
markd
  Fri Apr 22 09:27:25 2022 -0700
import of All GENCODE V40

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index b10ab12..296c163 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -1,488 +1,488 @@
 ####
 # build GENCODE tracks requires CCDS and markd python junk.
 # targets:
 #   all - do everything
 #   fetch - download gencode
 #   checkAttrs - check attribute conversion, so code can be updated to handle new biotypes
 #   mkTables - create table files
 #   loadTables - load tables
 #   checkSanity - do some checks on the tables
 #   cmpRelease - compare with previous release
 #   joinerCheck - run joinerCheck on gencode tabkes
 #
 # can use -j n to run multiple jobs in parallel.
 ####
 
 ##
 # make/bash robustness stuff
 ##
 .SECONDARY:
 host=$(shell hostname)
 ppid=$(shell echo $$PPID)
 tmpExt = ${host}.${ppid}.tmp
 SHELL = bash -e
 export SHELLOPTS=pipefail
 
 ##
 # programs, etc
 ##
 mach = $(shell uname -m)
 
 ##
 # Release info and files from Sanger.
 # BEGIN EDIT THESE EACH RELEASE
 ##
-#preRelease = no
-preRelease = yes
-#db = hg38
-db = hg19
+preRelease = no
+#preRelease = yes
+db = hg38
+#db = hg19
 #db = mm39
 #db = mm10
 ifeq (${db},mm10)
     grcRefAssembly = GRCm38
     verBase = M25
     prevVer = M24
     backmapTargetVer = M25
     ver = ${verBase}lift37
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${verBase}/GRCm38_mapping
     annGffTypeName = chr_patch_hapl_scaff.annotation
     isBackmap = yes
 else ifeq (${db},mm39)
     grcRefAssembly = GRCm39
     ver = M29
     prevVer = M28
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
     ver = 40
     prevVer = 39
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
 else ifeq (${db},hg19)
     grcRefAssembly = GRCh37
     verBase = 40
     ver = ${verBase}lift37
     prevVer = 38lift37
     backmapTargetVer = 19
     ftpReleaseSubdir = release_${verBase}/GRCh37_mapping
     gencodeOrg = Gencode_human
     annGffTypeName = annotation
     isBackmap = yes
 else
     $(error unimplement genome database: ${db})
 endif
 # END EDIT THESE EACH RELEASE
 
 
 ifeq (${preRelease},yes)
     # pre-release
     baseUrl = rsync://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre
 else
     # official release
     baseUrl = rsync://ftp.ebi.ac.uk/pub/databases/gencode
 endif
 
 rel = V${ver}
 releaseUrl = ${baseUrl}/${gencodeOrg}/${ftpReleaseSubdir}
 dataDir = data
 relDir = ${dataDir}/release_${ver}
 annotationGff = ${relDir}/gencode.v${ver}.${annGffTypeName}.gff3.gz
 pseudo2WayGff = ${relDir}/gencode.v${ver}.2wayconspseudos.gff3.gz
 polyAGff = ${relDir}/gencode.v${ver}.polyAs.gff3.gz
 
 gencodeBinDir = ${HOME}/kent/src/hg/makeDb/outside/gencode/bin
 gencodeMakeTracks = ${gencodeBinDir}/gencodeMakeTracks
 gencodeMakeAttrs = ${gencodeBinDir}/gencodeMakeAttrs
 gencodeExonSupportToTable = ${gencodeBinDir}/gencodeExonSupportToTable
 gencodeGxfToGenePred = ${gencodeBinDir}/gencodeGxfToGenePred
 gencodePolyaGxfToGenePred = ${gencodeBinDir}/gencodePolyaGxfToGenePred
 gencodeGxfToAttrs = ${gencodeBinDir}/gencodeGxfToAttrs
 buildGencodeToUcscLift = ${HOME}/kent/src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
 gencodeBackMapMetadataIds = ${gencodeBinDir}/gencodeBackMapMetadataIds
 encodeAutoSqlDir = ${HOME}/kent/src/hg/lib/encode
 
 ##
 # intermediate data not loaded into tracks
 ##
 gencodeGp = ${dataDir}/gencode.gp
 gencodeTsv = ${dataDir}/gencode.tsv
 gencodeToUcscChain = ${dataDir}/gencodeToUcsc.chain
 
 # flag indicating fetch was done
 fetchDone = ${relDir}/done
 
 ##
 # track and table data
 ##
 tableDir = tables
 tablePre = wgEncodeGencode
 
 # subset track and pattern for generate genePred and track names for each subset
 # obtained from gencode.v*.annotation.level_1_2.gtf, gencode.v*.annotation.level_3.gtf
 tableBasic = ${tablePre}Basic${rel}
 tableBasicGp = ${tableDir}/${tableBasic}.gp
 
 tableComp = ${tablePre}Comp${rel}
 tableCompGp = ${tableDir}/${tableComp}.gp
 
 tablePseudo = ${tablePre}PseudoGene${rel}
 tablePseudoGp = ${tableDir}/${tablePseudo}.gp
 
 tableAttrs = ${tablePre}Attrs${rel}
 tableAttrsTab = ${tableDir}/${tableAttrs}.tab
 
 tableTag = ${tablePre}Tag${rel}
 tableTagTab = ${tableDir}/${tableTag}.tab
 
 # obtained from gencode.v*.2wayconspseudos.GRCh37.gtf
 table2WayConsPseudo = ${tablePre}2wayConsPseudo${rel}
 table2WayConsPseudoGp = ${tableDir}/${table2WayConsPseudo}.gp
 
 # obtained from gencode.v*.polyAs.gtf
 tablePolyA = ${tablePre}Polya${rel}
 tablePolyAGp = ${tableDir}/${tablePolyA}.gp
 
 # other metadata
 tableGeneSourceMeta = ${relDir}/gencode.v${ver}.metadata.Gene_source.gz
 tableGeneSource = ${tablePre}GeneSource${rel}
 tableGeneSourceTab = ${tableDir}/${tableGeneSource}.tab
 
 tableTranscriptSourceMeta = ${relDir}/gencode.v${ver}.metadata.Transcript_source.gz
 tableTranscriptSource = ${tablePre}TranscriptSource${rel}
 tableTranscriptSourceTab = ${tableDir}/${tableTranscriptSource}.tab
 
 tableTranscriptSupportMeta = ${relDir}/gencode.v${ver}.metadata.Transcript_supporting_feature.gz
 tableTranscriptSupport = ${tablePre}TranscriptSupport${rel}
 tableTranscriptSupportTab = ${tableDir}/${tableTranscriptSupport}.tab
 
 tableExonSupportMeta = ${relDir}/gencode.v${ver}.metadata.Exon_supporting_feature.gz
 tableExonSupport = ${tablePre}ExonSupport${rel}
 tableExonSupportTab = ${tableDir}/${tableExonSupport}.tab
 
 ifeq (${gencodeOrg}, Gencode_human)
    tableGeneSymbolMeta = ${relDir}/gencode.v${ver}.metadata.HGNC.gz
 else
    tableGeneSymbolMeta = ${relDir}/gencode.v${ver}.metadata.MGI.gz
 endif
 tableGeneSymbol = ${tablePre}GeneSymbol${rel}
 tableGeneSymbolTab = ${tableDir}/${tableGeneSymbol}.tab
 
 tablePdbMeta = ${relDir}/gencode.v${ver}.metadata.PDB.gz
 tablePdb = ${tablePre}Pdb${rel}
 tablePdbTab = ${tableDir}/${tablePdb}.tab
 
 tablePubMedMeta = ${relDir}/gencode.v${ver}.metadata.Pubmed_id.gz
 tablePubMed = ${tablePre}PubMed${rel}
 tablePubMedTab = ${tableDir}/${tablePubMed}.tab
 
 tableRefSeqMeta = ${relDir}/gencode.v${ver}.metadata.RefSeq.gz
 tableRefSeq = ${tablePre}RefSeq${rel}
 tableRefSeqTab = ${tableDir}/${tableRefSeq}.tab
 
 tableSwissProtMeta = ${relDir}/gencode.v${ver}.metadata.SwissProt.gz
 tableTrEMBLMeta = ${relDir}/gencode.v${ver}.metadata.TrEMBL.gz
 tableUniProt = ${tablePre}UniProt${rel}
 tableUniProtTab = ${tableDir}/${tableUniProt}.tab
 
 tablePolyAFeatureMeta = ${relDir}/gencode.v${ver}.metadata.PolyA_feature.gz
 tablePolyAFeature = ${tablePre}PolyAFeature${rel}
 tablePolyAFeatureTab = ${tableDir}/${tablePolyAFeature}.tab
 
 tableAnnotationRemarkMeta = ${relDir}/gencode.v${ver}.metadata.Annotation_remark.gz
 tableAnnotationRemark = ${tablePre}AnnotationRemark${rel}
 tableAnnotationRemarkTab = ${tableDir}/${tableAnnotationRemark}.tab
 
 tableEntrezGeneMeta = ${relDir}/gencode.v${ver}.metadata.EntrezGene.gz
 tableEntrezGene = ${tablePre}EntrezGene${rel}
 tableEntrezGeneTab = ${tableDir}/${tableEntrezGene}.tab
 
 tableTranscriptionSupportLevel  = ${tablePre}TranscriptionSupportLevel${rel}
 tableTranscriptionSupportLevelTab = ${tableDir}/${tableTranscriptionSupportLevel}.tab
 
 genePredExtTables = ${tableBasic} ${tableComp} ${tablePseudo}
 genePredTables =
 tabTables = ${tableAttrs} ${tableTag} ${tableGeneSource} \
 	    ${tableTranscriptSource} ${tableTranscriptSupport} \
 	    ${tableGeneSymbol} ${tablePdb} ${tablePubMed} ${tableRefSeq} ${tableUniProt} \
 	    ${tableAnnotationRemark} ${tableEntrezGene}  ${tableTranscriptionSupportLevel}
 ifeq (${isBackmap}, yes)
     targetGencodeTsv = ${dataDir}/target-gencode.tsv
 else
     # these are not included in backmap releases
     genePredTables = ${table2WayConsPseudo}
     genePredExtTables += ${tablePolyA}
     tabTables += ${tableExonSupport}
 endif
 allTables = ${genePredExtTables} ${genePredTables} ${tabTables}
 
 # directory for flags indicating tables were loaded
 loadedDir = loaded
 
 # directory for output and flags for sanity checks
 checkDir = check
 
 all: fetch mkTables loadTables checkSanity cmpRelease listTables
 
 
 ##
 # fetch release, this doesn't get subdirectories so as not to copy the lift releases
 ##
 fetch: ${fetchDone}
 ${fetchDone}:
 	rsync -a --include='gencode.*' --exclude='*' '${releaseUrl}/' ${relDir}
 	touch $@
 
 ##
 # dependencies for files from release
 ##
 ${annotationGff}: ${fetchDone}
 ${pseudo2WayGff}: ${fetchDone}
 ${polyAGff}: ${fetchDone}
 ${tableGeneSourceMeta}: ${fetchDone}
 ${tableTranscriptSourceMeta}: ${fetchDone}
 ${tableTranscriptSupportMeta}: ${fetchDone}
 ${tableExonSupportMeta}: ${fetchDone}
 ${tableGeneSymbolMeta}: ${fetchDone}
 ${tablePdbMeta}: ${fetchDone}
 ${tablePubMedMeta}: ${fetchDone}
 ${tableRefSeqMeta}: ${fetchDone}
 ${tableSwissProtMeta}: ${fetchDone}
 ${tableTrEMBLMeta}: ${fetchDone}
 ${tablePolyAFeatureMeta}: ${fetchDone}
 ${tableAnnotationRemarkMeta}: ${fetchDone}
 ${tableEntrezGeneMeta}: ${fetchDone}
 
 ##
 # primary table files
 ##
 mkTables: ${genePredExtTables:%=${tableDir}/%.gp} ${genePredTables:%=${tableDir}/%.gp} \
 	  ${tabTables:%=${tableDir}/%.tab}
 
 # grab subset name from file pattern (this is what tr command below does)
 ${tableDir}/${tablePre}%${rel}.gp: ${gencodeGp} ${gencodeTsv}
 	@mkdir -p $(dir $@)
 	${gencodeMakeTracks}  $$(echo $* | tr A-Z a-z) ${gencodeGp} ${gencodeTsv} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${tableTagTab}: ${tableAttrsTab}
 ${tableTranscriptionSupportLevelTab}: ${tableAttrsTab}
 ${tableAttrsTab}: ${gencodeGp} ${gencodeTsv}
 	@mkdir -p $(dir $@)
 	${gencodeMakeAttrs} ${gencodeGp} ${gencodeTsv} $@.${tmpExt} ${tableTagTab}.${tmpExt} ${tableTranscriptionSupportLevelTab}.${tmpExt}
 	mv -f ${tableTranscriptionSupportLevelTab}.${tmpExt} ${tableTranscriptionSupportLevelTab}
 	mv -f ${tableTagTab}.${tmpExt} ${tableTagTab}
 	mv -f $@.${tmpExt} $@
 
 ${table2WayConsPseudoGp}: ${pseudo2WayGff}
 	@mkdir -p $(dir $@)
 	gff3ToGenePred -allowMinimalGenes $< $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${tablePolyAGp}: ${polyAGff} ${gencodeToUcscChain}
 	@mkdir -p $(dir $@)
 	${gencodePolyaGxfToGenePred} $< ${gencodeToUcscChain} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${tableUniProtTab}: ${tableSwissProtMeta} ${tableTrEMBLMeta} ${gencodeTsv}
 	@mkdir -p $(dir $@)
 	((${metaFilterCmdGz} ${tableSwissProtMeta} | tawk '{print $$0,"SwissProt"}') && (${metaFilterCmdGz}  ${tableTrEMBLMeta} | tawk '{print $$0,"TrEMBL"}')) | sort -k 1,1 > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${gencodeToUcscChain}:
 	@mkdir -p $(dir $@)
 	${buildGencodeToUcscLift} ${db} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 # other tab files, just copy to name following convention to make load rules
 # work
 ifeq (${isBackmap}, yes)
    metaFilterCmd = ${gencodeBackMapMetadataIds} ${db} ${gencodeTsv} ${targetGencodeTsv}
    metaFilterCmdGz = ${metaFilterCmd}
    metaFilterDepend = ${gencodeTsv} ${targetGencodeTsv}
 else
    metaFilterCmd = cat
    metaFilterCmdGz = zcat
    metaFilterDepend = ${gencodeTsv}
 endif
 define copyMetadataTabGz
 mkdir -p $(dir $@)
 ${metaFilterCmdGz} $< > $@.${tmpExt}
 mv -f $@.${tmpExt} $@
 endef
 define copyMetadataTab
 mkdir -p $(dir $@)
 ${metaFilterCmd} $< > $@.${tmpExt}
 mv -f $@.${tmpExt} $@
 endef
 
 ${tableGeneSourceTab}: ${tableGeneSourceMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableTranscriptSourceTab}: ${tableTranscriptSourceMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableTranscriptSupportTab}: ${tableTranscriptSupportMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableExonSupportTab}: ${tableExonSupportMeta} ${gencodeToUcscChain} ${metaFilterDepend}
 	@mkdir -p $(dir $@)
 	${gencodeExonSupportToTable} ${tableExonSupportMeta} ${gencodeToUcscChain} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 ${tableGeneSymbolTab}: ${tableGeneSymbolMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tablePdbTab}: ${tablePdbMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tablePubMedTab}: ${tablePubMedMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 ${tableRefSeqTab}: ${tableRefSeqMeta} ${metaFilterDepend}
 	${copyMetadataTabGz}
 
 # convert to zero-based, 1/2 open
 ${tablePolyAFeatureTab}: ${tablePolyAFeatureMeta} ${metaFilterDepend}
 	@mkdir -p $(dir $@)
 	zcat $< | tawk '{print $$1,$$2-1,$$3,$$4,$$5-1,$$6,$$7,$$8}' | sort -k 4,4 -k 5,5n > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 ${tableAnnotationRemarkTab}: ${tableAnnotationRemarkMeta} ${metaFilterDepend}
 	@mkdir -p $(dir $@)
 	${metaFilterCmdGz} $<  | tawk '{print $$1,gensub("\\\\n|\\\\","","g",$$2)}' | sort -k 1,1 > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 # drop ENSTR entries that are a hack to support PAR sequences in GTF
 ${tableEntrezGeneTab}: ${tableEntrezGeneMeta} ${metaFilterDepend}
 	@mkdir -p $(dir $@)
 	zcat $< | tawk '$$1!~/^ENSTR/' | sort -k 1,1 | ${metaFilterCmd} /dev/stdin > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ##
 # intermediate data for ensembl/havana, not loaded into databases
 ##
 ${gencodeGp}: ${annotationGff} ${gencodeToUcscChain}
 	@mkdir -p $(dir $@)
 	${gencodeGxfToGenePred} ${db} ${annotationGff} ${gencodeToUcscChain} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 	touch $@
 ${gencodeTsv}: ${annotationGff}
 	@mkdir -p $(dir $@)
 	${gencodeGxfToAttrs} ${annotationGff} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${targetGencodeTsv}:
 	@mkdir -p $(dir $@)
 	hgsql ${db}  -e 'select * from wgEncodeGencodeAttrsV${backmapTargetVer}' > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 
 # check attributes so code can be updated to handle new biotypes
 checkAttrs: ${annotationGff}
 	${gencodeGxfToAttrs} ${annotationGff} /dev/null
 
 ##
 # load tables
 #  browser commands use static tmp file name, so use lock file to serialize
 ##
 loadLock = flock load.lock
 
 loadTables: ${genePredExtTables:%=${loadedDir}/%.genePredExt.loaded} \
 	    ${genePredTables:%=${loadedDir}/%.genePred.loaded} \
 	    ${tabTables:%=${loadedDir}/%.tab.loaded}
 
 ${loadedDir}/%.genePredExt.loaded: ${tableDir}/%.gp
 	@mkdir -p $(dir $@)
 	${loadLock} hgLoadGenePred -genePredExt ${db} $* $<
 	touch $@
 
 ${loadedDir}/%.genePred.loaded: ${tableDir}/%.gp
 	@mkdir -p $(dir $@)
 	${loadLock} hgLoadGenePred ${db} $* $<
 	touch $@
 
 # generic tables
 ${loadedDir}/%.tab.loaded: ${tableDir}/%.tab
 	@mkdir -p $(dir $@)
 	${loadLock} hgLoadSqlTab ${db} $* ${encodeAutoSqlDir}/$(subst ${rel},,$*).sql $<
 	touch $@
 
 ##
 # sanity checks
 ##
 # check if the .incorrect files is empty
 define checkForIncorrect
 awk 'END{if (NR != 0) {print "Incorrect data, see " FILENAME>"/dev/stderr"; exit 1}}' $(basename $@).incorrect
 endef
 
 checkSanity:: ${checkDir}/${tableBasic}.checked ${checkDir}/${tableBasic}.pseudo.checked \
 	${checkDir}/${tableComp}.pseudo.checked
 
 # backmap does have all gene/transcript source entries.
 ifneq (${isBackmap},yes)
 checkSanity:: ${checkDir}/${tableGeneSource}.checked   ${checkDir}/${tableTranscriptSource}.checked
 endif
 
 # are gene source all in attrs
 ${checkDir}/${tableGeneSource}.checked: ${loadedDir}/${tableGeneSource}.tab.loaded ${loadedDir}/${tableAttrs}.tab.loaded
 	@mkdir -p $(dir $@)
 	hgsql -Ne 'select geneId from ${tableAttrs} where geneId not in (select geneId from ${tableGeneSource})' ${db} | sort -u >$(basename $@).incorrect
 	@$(checkForIncorrect)
 	touch $@
 
 # are transcript source all in attrs
 ${checkDir}/${tableTranscriptSource}.checked: ${loadedDir}/${tableTranscriptSource}.tab.loaded  ${loadedDir}/${tableAttrs}.tab.loaded
 	@mkdir -p $(dir $@)
 	hgsql -Ne 'select transcriptId from ${tableAttrs} where transcriptId not in (select transcriptId from ${tableTranscriptSource})' ${db} | sort -u >$(basename $@).incorrect
 	@$(checkForIncorrect)
 	touch $@
 
 # make sure all basic are in comprehensive
 ${checkDir}/${tableBasic}.checked: ${loadedDir}/${tableBasic}.genePredExt.loaded ${loadedDir}/${tableComp}.genePredExt.loaded
 	@mkdir -p $(dir $@)
 	hgsql -Ne 'select * from ${tableBasic} where name not in (select name from ${tableComp});' ${db} | sort -u >$(basename $@).incorrect
 	@$(checkForIncorrect)
 	touch $@
 
 # make there are no psuedo in basic
 ${checkDir}/${tableBasic}.pseudo.checked: ${loadedDir}/${tableBasic}.genePredExt.loaded ${loadedDir}/${tableAttrs}.tab.loaded
 	@mkdir -p $(dir $@)
 	hgsql -Ne 'select * from ${tableBasic}, ${tableAttrs} where name = transcriptId and geneType like "%pseudo%" and geneType != "polymorphic_pseudogene"' ${db} | sort -u >$(basename $@).incorrect
 	@$(checkForIncorrect)
 	touch $@
 
 # make there are no psuedo in comprehensive
 ${checkDir}/${tableComp}.pseudo.checked: ${loadedDir}/${tableComp}.genePredExt.loaded ${loadedDir}/${tableAttrs}.tab.loaded
 	@mkdir -p $(dir $@)
 	hgsql -Ne 'select * from ${tableComp}, ${tableAttrs} where name = transcriptId and geneType like "%pseudo%" and geneType != "polymorphic_pseudogene"' ${db} | sort -u >$(basename $@).incorrect
 	@$(checkForIncorrect)
 	touch $@
 
 # create table list to past into redmine
 listTables: tables.lst
 
 tables.lst: loadTables
 	hgsql -Ne 'show tables like "wgEncodeGencode%V${ver}"' ${db} >$@.tmp
 	mv -f $@.tmp $@
 
 
 ##
 # compare number of tracks with previous
 ##
 cmpRelease: gencode-cmp.tsv
 
 gencode-cmp.tsv: loadTables
 	@echo 'table	V${prevVer}	V${ver}	delta'  >$@.tmp
 	@for tab in ${allTables} ; do \
 	    prevTab=$$(echo "$$tab" | sed 's/V${ver}/V${prevVer}/g') ; \
 	    echo "$${tab}	"$$(hgsql -Ne "select count(*) from $${prevTab}" ${db})"	"$$(hgsql -Ne "select count(*) from $${tab}" ${db}) ; \
 	done | tawk '{print $$1, $$2, $$3, $$3-$$2}' >>$@.tmp
 	mv -f $@.tmp $@
 
 joinerCheck: loadTables
 	@mkdir -p check
 	for tbl in $$(hgsql -Ne 'show tables like "wgEncodeGencode%V${ver}"' ${db} | egrep -v 'wgEncodeGencode2wayConsPseudo|wgEncodeGencodePolya') ; do \
 	    echo  table=$$tbl; \
 	    runJoiner.csh ${db} $$tbl ~/kent/src/hg/makeDb/schema/all.joiner noTimes; \
 	    done >check/joiner.out 2>&1
 	if fgrep Error: check/joiner.out ; then false;  else true; fi
 
 
 clean:
 	rm -rf ${dataDir} ${tableDir} ${loadedDir} ${checkDir}